miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
1497	5'	-55.5	NC_001335.1	+	35303	0.66	0.662485
	Target:  5'- cUGGUgCGGGAacagcucCGGGAaCACCUCGGc -3' miRNA:   3'- aACCA-GCCCUa------GCUUUgGUGGAGCCa -5'
1497	5'	-55.5	NC_001335.1	+	14656	0.67	0.640356
	Target:  5'- cUGGUCGuGAUCGAagacggcgacAugCGCCUgGGg -3' miRNA:   3'- aACCAGCcCUAGCU----------UugGUGGAgCCa -5'
1497	5'	-55.5	NC_001335.1	+	5525	0.67	0.628167
	Target:  5'- cUGGggCGGGcUCGAcGCUgagucggcggcugACCUCGGUg -3' miRNA:   3'- aACCa-GCCCuAGCUuUGG-------------UGGAGCCA- -5'
1497	5'	-55.5	NC_001335.1	+	1174	0.67	0.618197
	Target:  5'- -cGGUucCGGGAcCGggGCCGCCUuuacuucccCGGc -3' miRNA:   3'- aaCCA--GCCCUaGCuuUGGUGGA---------GCCa -5'
1497	5'	-55.5	NC_001335.1	+	45460	0.68	0.5741
	Target:  5'- gUGGUCGGcg-CGGAACCACUUCc-- -3' miRNA:   3'- aACCAGCCcuaGCUUUGGUGGAGcca -5'
1497	5'	-55.5	NC_001335.1	+	1673	0.68	0.553391
	Target:  5'- -cGGUCGGGGUgucgccaccggcugaGAAGCCgACCUCGa- -3' miRNA:   3'- aaCCAGCCCUAg--------------CUUUGG-UGGAGCca -5'
1497	5'	-55.5	NC_001335.1	+	33320	1.05	0.001573
	Target:  5'- cUUGGUCGGGAUCGAAACCACCUCGGUg -3' miRNA:   3'- -AACCAGCCCUAGCUUUGGUGGAGCCA- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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